		Clinical Features	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_CHIERARCHICAL	
	nCNV (%)	nWild-Type	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q
1p gain	12 (3%)	451	NA	NA	NA	NA	9.3956e-05	0.0683	3.2784e-05	0.0242	0.024148	1	1	1	7.741e-09	6.08e-06	0.00082717	0.565	3.1443e-05	0.0232	0.0014437	0.961	0.00013655	0.098	0.0064145	1
1q gain	18 (4%)	445	NA	NA	NA	NA	0.00011016	0.0794	0.00013065	0.0939	0.43569	1	0.73827	1	0.00010733	0.0776	0.051277	1	0.00894	1	0.24994	1	0.00035284	0.246	0.20048	1
2p gain	11 (2%)	452	NA	NA	NA	NA	0.048877	1	0.046013	1	0.31113	1	0.43043	1	1.6747e-06	0.00126	0.13897	1	0.035588	1	0.15396	1	0.069525	1	0.1806	1
2q gain	10 (2%)	453	NA	NA	NA	NA	0.089793	1	0.031449	1	0.31113	1	0.43043	1	2.6037e-07	0.000199	0.23729	1	0.072846	1	0.21042	1	0.090928	1	0.21617	1
3p gain	11 (2%)	452	NA	NA	NA	NA	0.35148	1	0.1818	1	0.46396	1	0.44682	1	0.0077231	1	0.38843	1	0.14273	1	0.48082	1	0.26077	1	0.1806	1
3q gain	8 (2%)	455	NA	NA	NA	NA	0.21528	1	0.063978	1	0.055985	1	0.74032	1	0.00015127	0.108	0.36048	1	0.13473	1	0.47907	1	0.21142	1	0.36226	1
4p gain	12 (3%)	451	NA	NA	NA	NA	0.0067975	1	0.036101	1	0.032748	1	0.7866	1	0.0028807	1	0.010894	1	0.05632	1	0.15396	1	0.24029	1	0.070233	1
4q gain	5 (1%)	458	NA	NA	NA	NA	0.051273	1	0.12047	1	0.11301	1	0.66838	1	0.018476	1	0.58583	1	0.17669	1	0.48547	1	0.030316	1	0.035883	1
5p gain	9 (2%)	454	NA	NA	NA	NA	0.0027544	1	0.0047315	1	0.021682	1	1	1	5.7119e-05	0.0419	0.065242	1	0.0061718	1	0.10683	1	0.0059436	1	0.015216	1
5q gain	7 (2%)	456	NA	NA	NA	NA	0.0036085	1	0.0016571	1	NA	NA	NA	NA	0.010878	1	0.24231	1	0.011463	1	0.26681	1	0.014088	1	0.20013	1
6p gain	7 (2%)	456	NA	NA	NA	NA	0.0058309	1	0.048566	1	0.037839	1	0.46484	1	0.12747	1	0.030682	1	0.13749	1	0.019996	1	0.023116	1	0.20013	1
7p gain	117 (25%)	346	0.7446	1	0.64812	1	7.3336e-48	6.12e-45	5.9674e-24	4.9e-21	0.00087435	0.596	0.017696	1	8.504e-17	6.95e-14	1.3195e-06	0.000999	3.5253e-08	2.74e-05	0.0016992	1	6.7886e-10	5.37e-07	0.28912	1
7q gain	145 (31%)	318	0.7639	1	0.49526	1	3.8178e-45	3.18e-42	1.9185e-19	1.57e-16	0.0053135	1	0.038605	1	6.9359e-12	5.56e-09	6.8358e-07	0.00052	2.397e-07	0.000184	0.0020175	1	1.2774e-07	9.85e-05	0.57924	1
8p gain	39 (8%)	424	NA	NA	NA	NA	1.1518e-05	0.00857	0.014029	1	0.066672	1	0.56602	1	0.10868	1	0.10185	1	0.30782	1	0.47758	1	0.29598	1	0.21461	1
8q gain	49 (11%)	414	0.051852	1	0.30256	1	2.0038e-06	0.00151	0.0006511	0.448	0.012919	1	0.61811	1	0.0014262	0.953	0.021346	1	0.016635	1	0.47548	1	0.0053038	1	0.1892	1
9p gain	17 (4%)	446	NA	NA	NA	NA	0.0078385	1	0.14454	1	0.29435	1	0.81972	1	0.016702	1	0.3538	1	0.40573	1	0.43363	1	0.12569	1	0.24344	1
9q gain	22 (5%)	441	NA	NA	NA	NA	0.0033949	1	0.21899	1	0.25818	1	0.66107	1	0.0022224	1	0.36729	1	0.043564	1	0.36319	1	0.017273	1	0.025165	1
10p gain	47 (10%)	416	1	1	0.087863	1	1.625e-14	1.32e-11	6.1336e-13	4.94e-10	0.023328	1	0.54644	1	2.342e-09	1.85e-06	3.5535e-06	0.00267	0.014485	1	0.58181	1	0.016137	1	0.78889	1
10q gain	7 (2%)	456	NA	NA	NA	NA	0.00023412	0.165	0.23255	1	0.2669	1	0.46484	1	0.00029124	0.203	0.53957	1	0.0074508	1	0.42961	1	0.10833	1	0.72993	1
11p gain	29 (6%)	434	NA	NA	NA	NA	0.10951	1	0.0012085	0.811	0.026963	1	0.49573	1	0.0039547	1	0.019695	1	0.3694	1	0.77315	1	0.17091	1	0.62984	1
11q gain	50 (11%)	413	0.61538	1	0.11658	1	0.22891	1	0.018471	1	0.083688	1	0.14103	1	0.061382	1	0.072622	1	0.53936	1	0.78136	1	0.32032	1	0.7823	1
12p gain	30 (6%)	433	0.75385	1	0.087863	1	0.00020633	0.146	0.076419	1	0.26076	1	0.87476	1	0.14253	1	0.06208	1	0.029703	1	0.11083	1	0.02108	1	0.16629	1
12q gain	15 (3%)	448	NA	NA	NA	NA	0.0077095	1	0.03862	1	0.17332	1	1	1	0.030946	1	0.13233	1	0.043116	1	0.028976	1	0.0038505	1	0.028413	1
13q gain	5 (1%)	458	NA	NA	NA	NA	0.051273	1	0.13552	1	0.79242	1	1	1	0.62588	1	0.71914	1	0.76148	1	1	1	0.83655	1	1	1
14q gain	3 (1%)	460	NA	NA	NA	NA	1	1	1	1	NA	NA	NA	NA	0.9023	1	0.41577	1	0.37154	1	1	1	0.28139	1	0.60782	1
15q gain	10 (2%)	453	NA	NA	NA	NA	0.045693	1	0.029401	1	0.11375	1	0.46484	1	0.0048322	1	0.12514	1	0.024417	1	0.55595	1	0.10174	1	0.1535	1
16p gain	15 (3%)	448	NA	NA	NA	NA	0.22119	1	0.485	1	0.56065	1	0.65772	1	0.092931	1	0.13753	1	0.23592	1	0.21114	1	0.013619	1	0.0023444	1
16q gain	16 (3%)	447	NA	NA	NA	NA	0.033936	1	0.22851	1	0.46901	1	0.73827	1	0.0010084	0.681	0.16163	1	0.67891	1	0.29297	1	0.29549	1	0.0043942	1
17p gain	17 (4%)	446	NA	NA	NA	NA	0.5806	1	0.50536	1	0.34585	1	0.77096	1	0.00078601	0.538	0.27962	1	0.0013889	0.929	0.20889	1	0.0036202	1	0.051244	1
17q gain	19 (4%)	444	NA	NA	NA	NA	0.49962	1	0.33916	1	0.34585	1	0.77096	1	0.0023828	1	0.16558	1	0.0026308	1	0.085905	1	0.067541	1	0.035572	1
18p gain	15 (3%)	448	NA	NA	NA	NA	7.8966e-05	0.0577	0.010874	1	0.022636	1	0.20533	1	1.534e-10	1.22e-07	0.019448	1	0.72208	1	0.11838	1	0.41261	1	0.062963	1
18q gain	12 (3%)	451	NA	NA	NA	NA	0.00094008	0.637	0.0079647	1	0.08038	1	0.14214	1	3.4797e-08	2.71e-05	0.021448	1	0.3682	1	0.023383	1	0.19546	1	0.02173	1
19p gain	89 (19%)	374	0.22111	1	0.83612	1	1.4586e-09	1.15e-06	4.9723e-16	4.05e-13	0.61625	1	0.40581	1	3.2241e-10	2.56e-07	0.00021553	0.152	8.4558e-05	0.0616	0.54902	1	5.8007e-07	0.000443	0.52053	1
19q gain	24 (5%)	439	NA	NA	NA	NA	6.1238e-14	4.95e-11	3.9175e-15	3.18e-12	0.065771	1	0.18725	1	7.9428e-12	6.35e-09	0.00023711	0.166	3.6791e-09	2.9e-06	0.0035848	1	9.7219e-11	7.75e-08	0.182	1
20p gain	42 (9%)	421	NA	NA	NA	NA	5.9697e-12	4.79e-09	3.4539e-13	2.79e-10	0.0010111	0.681	0.1579	1	7.6235e-08	5.91e-05	0.0043993	1	2.6138e-06	0.00197	0.027702	1	1.739e-10	1.38e-07	0.21284	1
20q gain	42 (9%)	421	NA	NA	NA	NA	5.9697e-12	4.79e-09	5.6922e-14	4.61e-11	0.00089846	0.611	0.1097	1	7.1428e-10	5.64e-07	0.0006732	0.462	6.2835e-08	4.88e-05	0.0018911	1	2.1939e-12	1.77e-09	0.065571	1
21q gain	23 (5%)	440	NA	NA	NA	NA	0.020186	1	0.0019977	1	0.10983	1	0.53086	1	0.051397	1	0.92357	1	0.25171	1	0.86848	1	0.31768	1	0.72689	1
22q gain	17 (4%)	446	NA	NA	NA	NA	0.10928	1	0.00082004	0.561	1	1	0.5601	1	0.0037951	1	0.0079602	1	0.5193	1	0.47976	1	0.29576	1	0.3749	1
xq gain	35 (8%)	428	NA	NA	NA	NA	1.7869e-08	1.4e-05	8.2173e-07	0.000625	0.23894	1	0.72046	1	0.0098696	1	0.0011517	0.774	0.25813	1	0.34068	1	0.14256	1	0.41827	1
1p loss	168 (36%)	295	0.028572	1	0.00017271	0.123	6.3613e-47	5.3e-44	4.6023e-95	3.87e-92	0.0003111	0.217	0.142	1	9.1284e-52	7.64e-49	9.0562e-65	7.59e-62	1.6999e-22	1.39e-19	2.0828e-06	0.00157	7.0658e-27	5.82e-24	0.00012366	0.089
1q loss	23 (5%)	440	0.34359	1	0.14393	1	0.81124	1	0.12727	1	0.5517	1	0.54013	1	0.34089	1	0.30407	1	0.8487	1	0.66664	1	0.33625	1	0.23906	1
2p loss	19 (4%)	444	NA	NA	NA	NA	3.4511e-05	0.0254	0.068176	1	0.33106	1	1	1	0.11017	1	0.023264	1	0.1458	1	0.088329	1	0.74927	1	0.0082933	1
2q loss	18 (4%)	445	NA	NA	NA	NA	5.8245e-06	0.00435	0.0089558	1	0.0692	1	0.62827	1	0.082202	1	0.0055137	1	0.68248	1	0.43363	1	0.043781	1	0.004585	1
3p loss	25 (5%)	438	NA	NA	NA	NA	0.0025499	1	0.14594	1	0.0065168	1	0.48289	1	8.5982e-05	0.0626	0.0056695	1	0.023287	1	0.16468	1	0.02976	1	0.037668	1
3q loss	25 (5%)	438	0.17504	1	0.56068	1	0.005978	1	0.22079	1	0.25799	1	0.19137	1	0.00019962	0.142	0.068188	1	0.036388	1	0.11491	1	0.15078	1	0.037668	1
4p loss	67 (14%)	396	1	1	0.60733	1	0.016401	1	4.7718e-10	3.78e-07	0.42939	1	0.02872	1	3.5377e-08	2.75e-05	5.9383e-07	0.000452	0.0045997	1	0.065452	1	0.0018777	1	0.67552	1
4q loss	85 (18%)	378	1	1	0.19622	1	0.0038495	1	8.2886e-09	6.51e-06	0.26354	1	0.053242	1	1.2741e-07	9.84e-05	8.2297e-05	0.0601	0.00076286	0.523	0.014465	1	0.00040475	0.28	0.40883	1
5p loss	32 (7%)	431	0.7446	1	0.042206	1	3.676e-06	0.00276	0.0010659	0.717	0.84862	1	1	1	0.20614	1	0.045955	1	0.12965	1	0.56205	1	0.61281	1	0.18982	1
5q loss	29 (6%)	434	0.44623	1	0.018246	1	8.7829e-07	0.000667	0.0024214	1	0.021796	1	0.50804	1	1.6699e-07	0.000129	0.0041609	1	0.061966	1	0.10754	1	0.008037	1	0.00023046	0.162
6p loss	28 (6%)	435	NA	NA	NA	NA	0.037668	1	0.17771	1	0.18595	1	0.70781	1	0.342	1	0.54575	1	0.86936	1	0.5409	1	0.72751	1	0.45255	1
6q loss	57 (12%)	406	NA	NA	NA	NA	0.00062827	0.433	0.006974	1	0.25362	1	0.39785	1	0.15343	1	0.059337	1	0.25402	1	0.20723	1	0.098853	1	0.19066	1
7p loss	3 (1%)	460	NA	NA	NA	NA	0.45562	1	0.33193	1	NA	NA	NA	NA	0.93706	1	1	1	0.88711	1	1	1	0.9427	1	1	1
7q loss	3 (1%)	460	NA	NA	NA	NA	0.039781	1	0.33193	1	NA	NA	NA	NA	0.93706	1	1	1	0.56439	1	1	1	0.35052	1	1	1
8p loss	17 (4%)	446	0.61538	1	0.0013675	0.916	1.5039e-05	0.0112	9.5961e-05	0.0697	0.018505	1	0.62827	1	2.0814e-07	0.00016	0.0034664	1	2.9345e-05	0.0217	0.12818	1	2.3237e-05	0.0172	0.046286	1
8q loss	11 (2%)	452	NA	NA	NA	NA	0.00014248	0.102	1.5904e-05	0.0118	0.080624	1	0.74032	1	0.00010831	0.0782	0.021448	1	0.00028472	0.199	0.15396	1	0.00023077	0.162	0.1806	1
9p loss	107 (23%)	356	0.38387	1	0.26997	1	4.2154e-06	0.00315	0.00027447	0.192	0.031773	1	0.066426	1	0.00094386	0.639	0.028845	1	0.13001	1	0.84862	1	0.24754	1	0.54875	1
9q loss	46 (10%)	417	NA	NA	NA	NA	0.39265	1	0.42196	1	0.60738	1	0.50613	1	0.025779	1	0.47899	1	0.80746	1	0.69485	1	0.50615	1	0.58597	1
10p loss	76 (16%)	387	0.27077	1	0.56068	1	4.575e-40	3.79e-37	2.7548e-49	2.3e-46	2.5375e-07	0.000194	0.0023175	1	2.1549e-37	1.78e-34	1.0938e-08	8.56e-06	1.5811e-15	1.29e-12	2.8033e-05	0.0207	1.1275e-28	9.29e-26	0.0014335	0.956
10q loss	91 (20%)	372	0.27077	1	0.56068	1	1.4746e-33	1.22e-30	2.7543e-40	2.29e-37	1.3209e-06	0.000999	0.00087376	0.596	2.7616e-35	2.28e-32	4.6876e-11	3.74e-08	2.7647e-16	2.25e-13	4.1679e-06	0.00312	1.1873e-25	9.76e-23	0.0015608	1
11p loss	56 (12%)	407	1	1	0.013836	1	5.0232e-14	4.07e-11	1.2271e-10	9.77e-08	0.012703	1	0.5899	1	5.1515e-12	4.14e-09	8.7269e-09	6.84e-06	0.0027173	1	0.045836	1	0.0066317	1	0.0028726	1
11q loss	19 (4%)	444	NA	NA	NA	NA	0.00020156	0.143	0.00014685	0.105	0.017879	1	1	1	8.751e-08	6.77e-05	0.0042467	1	0.0022623	1	0.034241	1	0.0029323	1	0.0070532	1
12p loss	25 (5%)	438	NA	NA	NA	NA	0.031326	1	0.0069621	1	0.60346	1	0.50965	1	0.67309	1	0.079463	1	0.075698	1	0.35004	1	0.10656	1	0.67936	1
12q loss	47 (10%)	416	1	1	0.087863	1	2.1107e-08	1.65e-05	2.3596e-07	0.000181	0.58318	1	0.61259	1	0.036458	1	0.0003864	0.269	0.018961	1	0.44197	1	0.0015999	1	0.60465	1
13q loss	104 (22%)	359	0.1801	1	0.00061812	0.427	3.5021e-08	2.73e-05	0.027012	1	0.026271	1	0.49032	1	0.004681	1	0.011664	1	0.022631	1	0.23209	1	0.031098	1	0.070074	1
14q loss	70 (15%)	393	0.46711	1	0.47324	1	0.00039797	0.276	0.00015091	0.108	0.045908	1	0.14769	1	5.6952e-05	0.0418	0.011531	1	0.00062816	0.433	0.20839	1	0.00010356	0.0751	0.0052941	1
15q loss	45 (10%)	418	1	1	0.89231	1	0.06662	1	0.000585	0.405	0.27699	1	0.047616	1	0.0001043	0.0755	0.007513	1	0.095474	1	0.5177	1	0.0867	1	0.35845	1
16p loss	13 (3%)	450	NA	NA	NA	NA	0.0032142	1	0.060774	1	0.86477	1	0.44682	1	4.5318e-05	0.0333	1	1	0.3902	1	1	1	0.51922	1	0.18686	1
16q loss	20 (4%)	443	NA	NA	NA	NA	0.0037711	1	0.0024945	1	0.37381	1	0.21908	1	0.028165	1	0.39635	1	0.47168	1	0.45255	1	0.55632	1	0.47924	1
17p loss	14 (3%)	449	NA	NA	NA	NA	0.0046768	1	0.094484	1	1	1	0.60489	1	0.040861	1	0.094064	1	0.037773	1	0.014159	1	0.0085557	1	0.015901	1
17q loss	9 (2%)	454	NA	NA	NA	NA	0.057978	1	0.13796	1	0.83523	1	0.44682	1	0.4069	1	0.22724	1	0.057934	1	0.1753	1	0.095859	1	0.27124	1
18p loss	63 (14%)	400	0.32144	1	0.31568	1	0.43979	1	0.035151	1	0.57345	1	0.080072	1	0.56109	1	0.71924	1	0.036019	1	0.22201	1	0.55969	1	0.51917	1
18q loss	58 (13%)	405	0.34359	1	0.21231	1	0.1435	1	0.0018251	1	0.28483	1	0.20172	1	0.10215	1	0.18144	1	0.55918	1	0.35318	1	0.37156	1	0.61483	1
19p loss	21 (5%)	442	0.84676	1	0.31129	1	0.36553	1	0.75741	1	0.10256	1	0.66107	1	0.0082923	1	0.11305	1	0.47216	1	0.45255	1	0.75968	1	0.33531	1
19q loss	190 (41%)	273	0.18314	1	0.15869	1	1.1097e-35	9.18e-33	1.0677e-75	8.96e-73	0.038416	1	0.11799	1	6.8457e-42	5.69e-39	1.3275e-49	1.11e-46	1.8284e-16	1.49e-13	7.9416e-06	0.00592	3.0037e-20	2.46e-17	0.00025911	0.182
20p loss	5 (1%)	458	NA	NA	NA	NA	0.051273	1	0.13552	1	0.79242	1	1	1	1.0498e-06	0.000796	0.58583	1	0.21325	1	0.22497	1	0.14181	1	0.41676	1
20q loss	3 (1%)	460	NA	NA	NA	NA	0.15468	1	0.49376	1	NA	NA	NA	NA	0.00195	1	0.2926	1	0.27935	1	0.10657	1	0.11147	1	0.017334	1
21q loss	33 (7%)	430	0.61538	1	0.40684	1	0.00015928	0.114	0.0022137	1	0.46096	1	0.83387	1	0.0143	1	0.00097605	0.66	0.21184	1	0.012999	1	0.21889	1	0.073984	1
22q loss	50 (11%)	413	0.81538	1	0.10604	1	7.6935e-12	6.15e-09	1.0351e-07	8e-05	7.5833e-05	0.0555	0.040536	1	2.0184e-07	0.000155	0.00018654	0.132	0.072267	1	0.3882	1	0.0078331	1	0.048483	1
xq loss	60 (13%)	403	0.83946	1	0.022012	1	0.33762	1	0.00091077	0.618	0.047422	1	0.0088422	1	1.0461e-05	0.00779	0.00016191	0.115	0.0021919	1	0.93082	1	0.0049882	1	0.29823	1
